org.obolibrary.robot

Class QueryOperation

java.lang.Object

org.obolibrary.robot.QueryOperation

public class QueryOperation
extends Object

Query an ontology using SPARQL.

Author:

James A. Overton

Constructor Summary

Constructors

Constructor and Description
QueryOperation()

Method Summary

Modifier and Type	Method and Description
static org.semanticweb.owlapi.model.OWLOntology	convertModel(org.apache.jena.rdf.model.Model model) Deprecated. Use convertModel(Model, IOHelper, String)
static org.semanticweb.owlapi.model.OWLOntology	convertModel(org.apache.jena.rdf.model.Model model, IOHelper ioHelper, String catalogPath) Given a Model, an IOHelper, and a path to an XML catalog, convert the model to an OWLOntology object.
static int	countResults(org.apache.jena.query.ResultSet results) Count results.
static org.apache.jena.query.Dataset	createEmptyDataset()
static org.apache.jena.rdf.model.Model	execConstruct(org.apache.jena.sparql.core.DatasetGraph dsg, String query) Deprecated. use execConstruct(Dataset, String) instead.
static org.apache.jena.rdf.model.Model	execConstruct(org.apache.jena.query.Dataset dataset, String query) Execute a SPARQL CONSTRUCT query on a dataset and return a model.
static org.apache.jena.query.ResultSet	execQuery(org.apache.jena.sparql.core.DatasetGraph dsg, String query) Deprecated. use execQuery(Dataset, String) instead.
static org.apache.jena.query.ResultSet	execQuery(org.apache.jena.query.Dataset dataset, String query) Execute a SPARQL SELECT query on a dataset and return a result set.
static void	execUpdate(org.apache.jena.rdf.model.Model model, String updateString) Given a Model and a SPARQL update (as string), update the model.
static boolean	execVerify(org.apache.jena.sparql.core.DatasetGraph dsg, String ruleName, String query) Deprecated. use execVerify(Dataset, String, String) instead
static boolean	execVerify(org.apache.jena.query.Dataset dataset, String ruleName, String query) Given a dataset to query, a rule name, and the query string, execute the query over the dataset.
static boolean	execVerify(Map<File,Tuple<org.apache.jena.query.ResultSetRewindable,OutputStream>> queriesResults) Deprecated. previously used as test method.
static String	getDefaultFormatName(org.apache.jena.query.Query query) Given a SPARQL query, return its default file format as a string.
static String	getDefaultFormatName(String query) Given a SPARQL query, return its default file format as a string.
static org.apache.jena.riot.Lang	getFormatLang(String formatName) Convert a format name string to a language code.
static String	getQueryTypeName(String queryString) Given a SPARQL query, return its type as a string: ASK, CONSTRUCT, DESCRIBE, or SELECT.
static boolean	hasResult(org.apache.jena.rdf.model.Model result) If a model has statements, return true, otherwise false.
static boolean	hasResult(org.apache.jena.query.ResultSet result) If a result set has results, return true, otherwise false.
static org.apache.jena.sparql.core.DatasetGraph	loadOntology(org.semanticweb.owlapi.model.OWLOntology ontology) Deprecated. use loadOntologyAsDataset(OWLOntology) instead.
static org.apache.jena.query.Dataset	loadOntologyAsDataset(org.semanticweb.owlapi.model.OWLOntology ontology) Given an ontology, return a dataset containing that ontology as the only graph.
static org.apache.jena.query.Dataset	loadOntologyAsDataset(org.semanticweb.owlapi.model.OWLOntology ontology, boolean useGraphs) Given an ontology and a boolean indicating if imports should be included as graphs, return a dataset either with just the ontology, or the ontology and its imports as separate graphs.
static org.apache.jena.rdf.model.Model	loadOntologyAsModel(org.semanticweb.owlapi.model.OWLOntology ontology) Given an OWLOntology, return the Model representation of the axioms.
static org.apache.jena.query.Dataset	loadTriplesAsDataset(String inputPath, String tdbDir) Deprecated. moved to IOHelper.loadToTDBDataset(String, String)
static boolean	maybeWriteResult(org.apache.jena.rdf.model.Model result, String formatName, OutputStream output) If a model has statements, write to the output stream and return true.
static boolean	maybeWriteResult(org.apache.jena.query.ResultSet result, String formatName, OutputStream output) If a result set has results, write to the output stream and return true.
static void	runConstruct(org.apache.jena.query.Dataset dataset, String query, File output, org.apache.jena.riot.Lang outputFormat) Run a CONSTRUCT query and write the result to a file.
static void	runQuery(org.apache.jena.sparql.core.DatasetGraph dsg, String query, File output, org.apache.jena.riot.Lang outputFormat) Deprecated. use runQuery(Dataset, String, File, Lang) instead.
static void	runQuery(org.apache.jena.query.Dataset dataset, String query, File output, org.apache.jena.riot.Lang outputFormat) Run a SELECT query on a dataset and write the result to a file.
static boolean	runSparqlQuery(org.apache.jena.sparql.core.DatasetGraph dsg, String query, String formatName, OutputStream output) Deprecated. use runSparqlQuery(Dataset, String, String, OutputStream) instead.
static boolean	runSparqlQuery(org.apache.jena.query.Dataset dataset, String queryString, String formatName, OutputStream output) Given a dataset, a query string, a format name, and an output stream, run the SPARQL query over the named graphs and write the output to the stream.
static boolean	runSparqlQuery(org.apache.jena.query.QueryExecution qExec, String formatName, OutputStream output) Given a query execution, a format name, and an output stream, run the query and write to output.
static void	runUpdate(org.apache.jena.rdf.model.Model model, String updateString, File output, org.apache.jena.riot.Lang outputFormat) Given a Model, a SPARQL update string, an output stream, and the output format, update the model and write it to the output.
static boolean	runVerify(org.apache.jena.sparql.core.DatasetGraph dsg, String ruleName, String query, Path outputPath, org.apache.jena.riot.Lang outputFormat) Deprecated. use runVerify(Dataset, String, String, Path, Lang) instead.
static boolean	runVerify(org.apache.jena.query.Dataset dataset, String ruleName, String query, Path outputPath, org.apache.jena.riot.Lang outputFormat) Run a SELECT query over the union of named graphs in a dataset and write the result to a file.
static void	writeResult(boolean result, OutputStream output) Write a boolean result to an output stream.
static void	writeResult(org.apache.jena.rdf.model.Model model, org.apache.jena.riot.Lang format, OutputStream output) Write a model to an output stream.
static void	writeResult(org.apache.jena.rdf.model.Model model, String formatName, OutputStream output) Write a model to an output stream.
static void	writeResult(org.apache.jena.query.ResultSet resultSet, org.apache.jena.riot.Lang format, OutputStream output) Write a result set to an output stream.
static void	writeResult(org.apache.jena.query.ResultSet resultSet, String formatName, OutputStream output) Write a result set to an output stream.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

QueryOperation

public QueryOperation()

Method Detail

loadOntology

@Deprecated
public static org.apache.jena.sparql.core.DatasetGraph loadOntology(org.semanticweb.owlapi.model.OWLOntology ontology)
                                                                         throws org.semanticweb.owlapi.model.OWLOntologyStorageException

Deprecated. use loadOntologyAsDataset(OWLOntology) instead.

Load an ontology into a DatasetGraph. The ontology is not changed.

Parameters:

ontology - The ontology to load into the graph

Returns:

A new DatasetGraph with the ontology loaded into the default graph

Throws:

org.semanticweb.owlapi.model.OWLOntologyStorageException - rarely

loadOntologyAsDataset

public static org.apache.jena.query.Dataset loadOntologyAsDataset(org.semanticweb.owlapi.model.OWLOntology ontology)
                                                           throws org.semanticweb.owlapi.model.OWLOntologyStorageException

Given an ontology, return a dataset containing that ontology as the only graph.

Parameters:

ontology - ontology to query

Returns:

dataset to query

Throws:

org.semanticweb.owlapi.model.OWLOntologyStorageException - on issue converting ontology Jena model

loadOntologyAsDataset

public static org.apache.jena.query.Dataset loadOntologyAsDataset(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                  boolean useGraphs)
                                                           throws org.semanticweb.owlapi.model.OWLOntologyStorageException

Given an ontology and a boolean indicating if imports should be included as graphs, return a dataset either with just the ontology, or the ontology and its imports as separate graphs.

Parameters:

ontology - ontology to query

useGraphs - if true, load imports as separate graphs

Returns:

dataset to query

Throws:

org.semanticweb.owlapi.model.OWLOntologyStorageException - on issue converting ontology Jena model

loadOntologyAsModel

public static org.apache.jena.rdf.model.Model loadOntologyAsModel(org.semanticweb.owlapi.model.OWLOntology ontology)
                                                           throws org.semanticweb.owlapi.model.OWLOntologyStorageException

Given an OWLOntology, return the Model representation of the axioms.

Parameters:

ontology - OWLOntology to convert to Model

Returns:

Model of axioms (imports ignored)

Throws:

org.semanticweb.owlapi.model.OWLOntologyStorageException - on issue rendering ontology to triples

loadTriplesAsDataset

@Deprecated
public static org.apache.jena.query.Dataset loadTriplesAsDataset(String inputPath,
                                                                             String tdbDir)

Deprecated. moved to IOHelper.loadToTDBDataset(String, String)

Given a path to an RDF/XML or TTL file and a RDF language, load the file as the default model of a TDB dataset backed by a directory to improve processing time. Return the new dataset.

WARNING - this creates a directory at given tdbDir location!

Parameters:

inputPath - input path of RDF/XML or TTL file

tdbDir - location to put TDB mappings

Returns:

Dataset instantiated with triples

convertModel

@Deprecated
public static org.semanticweb.owlapi.model.OWLOntology convertModel(org.apache.jena.rdf.model.Model model)
                                                                         throws org.semanticweb.owlapi.model.OWLOntologyCreationException

Deprecated. Use convertModel(Model, IOHelper, String)

Given a Model, return the OWLOntology representation of the axioms.

Parameters:

model - Model to convert to OWLOntology

Returns:

OWLOntology of axioms

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException - on issue loading ontology from byte array

convertModel

public static org.semanticweb.owlapi.model.OWLOntology convertModel(org.apache.jena.rdf.model.Model model,
                                                                    IOHelper ioHelper,
                                                                    String catalogPath)
                                                             throws IOException

Given a Model, an IOHelper, and a path to an XML catalog, convert the model to an OWLOntology object.

Parameters:

model - Model to convert to OWLOntology

ioHelper - IOHelper to load ontology

catalogPath - String path to XML catalog

Returns:

OWLOntology object version of model

Throws:

IOException - on issue loading ontology

countResults

public static int countResults(org.apache.jena.query.ResultSet results)

Count results.

Parameters:

results - The result set to count.

Returns:

the size of the result set

createEmptyDataset

public static org.apache.jena.query.Dataset createEmptyDataset()

execConstruct

@Deprecated
public static org.apache.jena.rdf.model.Model execConstruct(org.apache.jena.sparql.core.DatasetGraph dsg,
                                                                        String query)

Deprecated. use execConstruct(Dataset, String) instead.

Execute a SPARQL CONSTRUCT query on a graph and return the model.

Parameters:

dsg - the graph to construct in

query - the SPARQL construct query string

Returns:

the result Model

execConstruct

public static org.apache.jena.rdf.model.Model execConstruct(org.apache.jena.query.Dataset dataset,
                                                            String query)

Execute a SPARQL CONSTRUCT query on a dataset and return a model.

Parameters:

dataset - the Dataset to construct in

query - the SPARQL construct query string

Returns:

the result Model

execQuery

@Deprecated
public static org.apache.jena.query.ResultSet execQuery(org.apache.jena.sparql.core.DatasetGraph dsg,
                                                                    String query)
                                                             throws IOException

Deprecated. use execQuery(Dataset, String) instead.

Execute a SPARQL SELECT query on a graph and return a result set.

Parameters:

dsg - the graph to query

query - the SPARQL query string

Returns:

the result set

Throws:

IOException - on query parse error

execQuery

public static org.apache.jena.query.ResultSet execQuery(org.apache.jena.query.Dataset dataset,
                                                        String query)
                                                 throws IOException

Execute a SPARQL SELECT query on a dataset and return a result set.

Parameters:

dataset - the Dataset to query over

query - the SPARQL query string

Returns:

the result set

Throws:

IOException - on query parse error

execUpdate

public static void execUpdate(org.apache.jena.rdf.model.Model model,
                              String updateString)

Given a Model and a SPARQL update (as string), update the model.

Parameters:

model - Model to update

updateString - SPARQL update

execVerify

@Deprecated
public static boolean execVerify(Map<File,Tuple<org.apache.jena.query.ResultSetRewindable,OutputStream>> queriesResults)
                                      throws IOException

Deprecated. previously used as test method.

Execute a verification. Writes to STDERR.

Parameters:

queriesResults - a map from files to query results and output streams

Returns:

true if there are any violations

Throws:

IOException - on file issues

execVerify

@Deprecated
public static boolean execVerify(org.apache.jena.sparql.core.DatasetGraph dsg,
                                             String ruleName,
                                             String query)
                                      throws IOException

Deprecated. use execVerify(Dataset, String, String) instead

Execute a SPARQL query and return true if there are any results, false otherwise.

Parameters:

dsg - the graph to query over

ruleName - name of rule to verify

query - the SPARQL query string

Returns:

true if the are results, false otherwise

Throws:

IOException - on query parse error

execVerify

public static boolean execVerify(org.apache.jena.query.Dataset dataset,
                                 String ruleName,
                                 String query)
                          throws IOException

Given a dataset to query, a rule name, and the query string, execute the query over the dataset.

Parameters:

dataset - Dataset to query

ruleName - name of rule to verify

query - the SPARQL query string

Returns:

true if there are results, false otherwise

Throws:

IOException - on query parse error

getDefaultFormatName

public static String getDefaultFormatName(String query)

Given a SPARQL query, return its default file format as a string.

Parameters:

query - the SPARQL query string

Returns:

the format name

getDefaultFormatName

public static String getDefaultFormatName(org.apache.jena.query.Query query)
                                   throws IllegalArgumentException

Given a SPARQL query, return its default file format as a string.

Parameters:

query - the SPARQL query

Returns:

the format name

Throws:

IllegalArgumentException - on bad query

getFormatLang

public static org.apache.jena.riot.Lang getFormatLang(String formatName)

Convert a format name string to a language code.

Parameters:

formatName - the format name as a string

Returns:

the format language code or null

getQueryTypeName

public static String getQueryTypeName(String queryString)

Given a SPARQL query, return its type as a string: ASK, CONSTRUCT, DESCRIBE, or SELECT.

Parameters:

queryString - the SPARQL query string

Returns:

the query type string

Throws:

IllegalArgumentException - on bad query

hasResult

public static boolean hasResult(org.apache.jena.query.ResultSet result)

If a result set has results, return true, otherwise false.

Parameters:

result - the results to write

Returns:

true if there are results, false otherwise

hasResult

public static boolean hasResult(org.apache.jena.rdf.model.Model result)

If a model has statements, return true, otherwise false.

Parameters:

result - the results to write

Returns:

true if there are statements, false otherwise

maybeWriteResult

public static boolean maybeWriteResult(org.apache.jena.query.ResultSet result,
                                       String formatName,
                                       OutputStream output)

If a result set has results, write to the output stream and return true. Otherwise return false.

Parameters:

result - the results to write

formatName - the name of the language to write in

output - the output stream to write to

Returns:

true if there were results, false otherwise

maybeWriteResult

public static boolean maybeWriteResult(org.apache.jena.rdf.model.Model result,
                                       String formatName,
                                       OutputStream output)

If a model has statements, write to the output stream and return true. Otherwise return false.

Parameters:

result - the Model to write

formatName - the name of the language to write in

output - the output stream to write to

Returns:

true if there were statements, false otherwise

runConstruct

public static void runConstruct(org.apache.jena.query.Dataset dataset,
                                String query,
                                File output,
                                org.apache.jena.riot.Lang outputFormat)
                         throws FileNotFoundException

Run a CONSTRUCT query and write the result to a file.

Parameters:

dataset - the Dataset to construct in.

query - The SPARQL construct query string.

output - The file to write to.

outputFormat - The file format.

Throws:

FileNotFoundException - if output file is not found

runQuery

@Deprecated
public static void runQuery(org.apache.jena.sparql.core.DatasetGraph dsg,
                                        String query,
                                        File output,
                                        org.apache.jena.riot.Lang outputFormat)
                                 throws IOException

Deprecated. use runQuery(Dataset, String, File, Lang) instead.

Run a SELECT query on a graph and write the results to a file.

Parameters:

dsg - the graph to query

query - The SPARQL query string.

output - The file to write to.

outputFormat - The file format.

Throws:

IOException - if output file is not found or query cannot be parsed

runQuery

public static void runQuery(org.apache.jena.query.Dataset dataset,
                            String query,
                            File output,
                            org.apache.jena.riot.Lang outputFormat)
                     throws IOException

Run a SELECT query on a dataset and write the result to a file.

Parameters:

dataset - The dataset to query over.

query - The SPARQL query string.

output - The file to write to.

outputFormat - The file format.

Throws:

IOException - if output file is not found or query cannot be parsed

runSparqlQuery

@Deprecated
public static boolean runSparqlQuery(org.apache.jena.sparql.core.DatasetGraph dsg,
                                                 String query,
                                                 String formatName,
                                                 OutputStream output)
                                          throws IOException

Deprecated. use runSparqlQuery(Dataset, String, String, OutputStream) instead.

Run a SPARQL query and return true if there were results, false otherwise.

Parameters:

dsg - the graph to query over

query - the SPARQL query string

formatName - the name of the output format

output - the OutputStream to write to

Returns:

true if results, false if otherwise

Throws:

IOException - on issue parsing query

runSparqlQuery

public static boolean runSparqlQuery(org.apache.jena.query.Dataset dataset,
                                     String queryString,
                                     String formatName,
                                     OutputStream output)
                              throws IOException

Given a dataset, a query string, a format name, and an output stream, run the SPARQL query over the named graphs and write the output to the stream.

Parameters:

dataset - Dataset to query over

queryString - query to run

formatName - format of output

output - output stream to write to

Returns:

true if successful

Throws:

IOException - on issue parsing query

runSparqlQuery

public static boolean runSparqlQuery(org.apache.jena.query.QueryExecution qExec,
                                     String formatName,
                                     OutputStream output)

Given a query execution, a format name, and an output stream, run the query and write to output.

Parameters:

qExec - QueryExecution to run

formatName - format of output

output - output stream to write to

Returns:

true if there are results

runUpdate

public static void runUpdate(org.apache.jena.rdf.model.Model model,
                             String updateString,
                             File output,
                             org.apache.jena.riot.Lang outputFormat)
                      throws FileNotFoundException

Given a Model, a SPARQL update string, an output stream, and the output format, update the model and write it to the output.

Parameters:

model - Model to update

updateString - SPARQL update

output - output stream to write to

outputFormat - the file format

Throws:

FileNotFoundException - if output file cannot be found

runVerify

@Deprecated
public static boolean runVerify(org.apache.jena.sparql.core.DatasetGraph dsg,
                                            String ruleName,
                                            String query,
                                            Path outputPath,
                                            org.apache.jena.riot.Lang outputFormat)
                                     throws IOException

Deprecated. use runVerify(Dataset, String, String, Path, Lang) instead.

Run a SELECT query over the graph and write the result to a file. Prints violations to STDERR.

Parameters:

dsg - The graph to query over.

ruleName - name of the rule

query - The SPARQL query string.

outputPath - The file path to write to, if there are results

outputFormat - The file format.

Returns:

true if the are results (so file is written), false otherwise

Throws:

IOException - if output file is not found or query cannot be parsed

runVerify

public static boolean runVerify(org.apache.jena.query.Dataset dataset,
                                String ruleName,
                                String query,
                                Path outputPath,
                                org.apache.jena.riot.Lang outputFormat)
                         throws IOException

Run a SELECT query over the union of named graphs in a dataset and write the result to a file. Prints violations to STDERR.

Parameters:

dataset - The dataset to query over.

ruleName - The name of the rule to verify.

query - The SPARQL query string.

outputPath - The file path to write to, if there are results

outputFormat - The file format.

Returns:

true if the are results (so file is written), false otherwise

Throws:

IOException - if output file is not found or query cannot be parsed

writeResult

public static void writeResult(boolean result,
                               OutputStream output)

Write a boolean result to an output stream.

Parameters:

result - the boolean to write

output - the output stream to write to

writeResult

public static void writeResult(org.apache.jena.query.ResultSet resultSet,
                               String formatName,
                               OutputStream output)

Write a result set to an output stream.

Parameters:

resultSet - the results to write

formatName - the name of the language to write in

output - the output stream to write to

writeResult

public static void writeResult(org.apache.jena.query.ResultSet resultSet,
                               org.apache.jena.riot.Lang format,
                               OutputStream output)

Write a result set to an output stream.

Parameters:

resultSet - the results to write

format - the language to write in (if null, CSV)

output - the output stream to write to

writeResult

public static void writeResult(org.apache.jena.rdf.model.Model model,
                               String formatName,
                               OutputStream output)

Write a model to an output stream.

Parameters:

model - the Model to write

formatName - the name of the language to write in

output - the output stream to write to

writeResult

public static void writeResult(org.apache.jena.rdf.model.Model model,
                               org.apache.jena.riot.Lang format,
                               OutputStream output)

Write a model to an output stream.

Parameters:

model - the Model to write

format - the language to write in (if null, TTL)

output - the output stream to write to